Contacts of the strand formed by residues 164 - 170 (chain A) in PDB entry 3S3J
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLN 164 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A GLU* 5.0 1.0 - - - +
162A THR* 3.3 23.6 - - - +
163A GLN* 1.3 96.4 + - - +
165A GLY* 1.3 59.3 + - - +
180A TRP 3.2 12.3 - - - +
181A ASN* 3.0 29.0 + - + +
182A PHE* 4.1 5.5 - - - -
289A ARG* 4.8 1.7 + - - -
429A LYS* 4.6 1.2 - - - -
707A GOL 3.3 14.4 + - - +
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Residues in contact with GLY 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A GLU* 5.6 0.4 - - - -
164A GLN* 1.3 76.4 - - - +
166A PHE* 1.3 66.6 + - - -
179A PRO* 3.5 5.2 - - - +
180A TRP* 3.0 31.2 + - - -
182A PHE* 3.8 15.5 - - - -
289A ARG* 5.9 0.4 - - - -
429A LYS* 3.8 16.8 - - - -
707A GOL 4.9 0.9 - - - -
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Residues in contact with PHE 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A GLY* 1.3 79.2 - - - -
167A ILE* 1.3 67.4 + - - +
168A TYR* 3.9 33.8 - - + +
177A ASN* 2.9 36.3 - - + -
178A ILE 3.4 1.6 - - - +
179A PRO* 3.9 18.4 - - + -
182A PHE* 5.0 2.9 - - - -
297A VAL* 5.0 7.4 - - - +
429A LYS* 3.7 32.6 + - + +
434A ASP* 3.6 48.9 - - + -
707A GOL 5.6 0.9 - - - -
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Residues in contact with ILE 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A PHE* 1.3 80.5 - - - +
168A TYR* 1.3 71.2 + - - +
169A GLN* 3.8 3.9 + - + +
177A ASN* 3.7 0.2 - - - -
178A ILE* 2.9 43.0 + - + +
180A TRP* 3.8 29.6 - - + -
182A PHE* 4.6 4.3 - - + -
278A TRP* 3.7 33.4 - - + +
282A ALA* 3.5 34.8 - - + -
297A VAL* 4.2 28.7 - - + -
336A CYS* 4.5 2.2 - - - -
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Residues in contact with TYR 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A PHE* 3.9 28.6 - - + +
167A ILE* 1.3 75.7 - - - +
169A GLN* 1.3 63.5 - - - +
175A ILE* 3.8 19.5 - - + -
176A LYS 3.4 1.1 - - - -
177A ASN* 3.8 24.7 - - + -
297A VAL* 5.6 1.8 - - - +
299A THR* 2.7 37.7 + - - +
301A TYR* 3.4 14.8 - - - +
336A CYS* 3.9 6.9 - - - -
427A SER* 4.3 13.0 - - - -
428A THR* 3.7 13.5 - - - -
429A LYS* 3.6 27.9 - - - +
435A GLU 3.4 24.1 + - - -
436A ARG* 3.4 25.1 - - + -
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Residues in contact with GLN 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A ILE* 4.2 6.5 - - + +
168A TYR* 1.3 80.1 - - - +
170A GLY* 1.3 63.0 + - - +
171A SER 3.6 0.5 + - - -
175A ILE* 3.8 0.2 - - - -
176A LYS* 2.7 42.7 + - - +
178A ILE* 3.1 24.2 - - - +
252A MET* 5.9 0.2 - - - +
278A TRP* 3.2 50.1 - - + +
301A TYR* 2.6 25.3 + - - -
334A PHE* 3.8 19.1 - - + -
277B PHQ 2.7 32.1 - - + -
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Residues in contact with GLY 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A GLN* 1.3 78.0 - - - +
171A SER* 1.3 61.6 + - - -
174A PHE* 3.6 8.3 - - - -
176A LYS* 4.4 6.1 - - - -
301A TYR* 3.9 1.8 - - - -
333A ASN* 3.5 12.2 + - - +
334A PHE* 3.2 21.5 - - - +
277B PHQ 3.4 22.1 - - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il